Eficiência dos métodos de otimização simulatedannealin, delineação rápida em cadeia e ramos e conexões para construção de mapas genéticos / Efficiency of the simulated annealing, rapid chain delineation, and branch and bounds optimization methods in genetic mapping

Um mapa genético é um diagrama onde são representados os genes com suas respectivas posições no cromossomo. Eles são essenciais para o procedimento de localização de genes envolvidos no controle genético de caracteres quantitativos ou no controle de outros caracteres de interesse econômico. No presente trabalho avalia-se, via simulação computacional de dados, a eficiência dos algoritmos simulated annealing, delineação rápida em cadeia e ramos e conexões, para a construção de mapas genéticos. Nas condições avaliadas, o algoritmo ramos e conexões foi o mais rápido, sendo que tanto este, quanto a delineação rápida em cadeia apresentaram 100 por cento de eficiência. A eficiência do simulated annealing para ordenação de marcadores variou com o número de marcadores, para 5 e 10 foi de 100 por cento, para 15 99,8 por cento e com 20 marcadores a eficiência obtida foi de 99,2 por cento.

The efficiency of Simulated Annealing (SA), Rapid Chain Delineation (RCD) and Branch and Bounds (BB) algorithms was evaluated by a Monte Carlo method. Regarding the conditions appraised the Branch and Bounds showed to be the fastest among them. Both RCD and BB were 100 percent efficient. The efficiency of SA depends on the length of the linkage group to be ordered. For 5 and 10 the efficiency was 100 percent, for 15 it was 99.8 percent and for 20 it was 99.2 percent.

Mapping and validation of quantitative trait loci for resistance to Cercospora zeae-maydis infection in tropical maize (Zea mays L.).

Breeding for resistance to gray leaf spot, caused by Cercospora zeae-maydis (Cz) is paramount for many maize environments, in particular under warm and humid growing conditions. In this study, we mapped and characterized quantitative trait loci (QTL) involved in the resistance of maize against Cz. We confirmed the impact of the QTL on disease severity using near-isogenic lines (NILs), and estimated their effects on three major agronomic traits using their respective near isogenic hybrids (NIHs), which we obtained by crossing the NILs with an inbred from a complementary heterotic pool. We further validated three of the four QTL that were mapped using the Multiple Interval Mapping approach and showed LOD values>2.5. NILs genotype included all combinations between favorable alleles of the two QTL located in chromosome 1 (Q1 in bin 1.05 and Q2 in bin 1.07), and the allele in chromosome 3 (Q3 in bin 3.07). Each of the three QTL separately significantly reduced the severity of Cz. However, we found an unfavorable epistatic interaction between Q1 and Q2: presence of the favorable allele at one of the QTL allele effectively nullified the effect of the favorable allele at the other. In contrast, the interaction between Q2 and Q3 was additive, promoting the reduction of the severity to a greater extent than the sum of their individual effects. When evaluating the NIH we found significant individual effects for Q1 and Q3 on gray leaf spot severity, for Q2 on stalk lodging and grain yield, and for Q3 on grain moisture and stalk lodging. We detected significant epitasis between Q1 and Q2 for grain moisture and between Q1 and Q3 for stalk lodging. These results suggest that the combination of QTL impacts the effectiveness of marker-assisted selection procedures in commercial product development programs.

Genotypic interactions of renin-angiotensin system genes in myocardial infarction.

BACKGROUND: Three-gene interactions among the genetic polymorphisms of the renin-angiotensin system (RAS) associated with acute myocardial infarction (AMI) have not been examined in a single population. We hypothesized that all types of gene-to-gene associations may occur in AMI, but that some will have a higher risk, depending on the gene frequencies. METHODS: Polymorphisms of the AGT (M235T), ACE (I/D) and AGTR1 (A1166C) genes in AMI patients and controls were analyzed using the polymerase chain reaction. Classic coronary risk factors were analyzed in all individuals. RESULTS: Logistic regression analysis of these factors and the genetic polymorphisms demonstrated that smoking, family history of CAD, arterial hypertension and total cholesterol were the most significant contributors to AMI. The genotypic frequencies for all three genes alone were similar between the infarction and control groups, with no increased risk of developing AMI. Double homozygous combinations for normal alleles (MM of AGT, II of ACE and AA of AGTR1) had a lower risk of AMI (odds ratio<0.38), indicating a protective effect in these individuals. In genotypic combinations that included at least one unfavorable allele, the risk (odds ratio) of developing AMI was 2.92, 2.63 and 2.68 for AGT vs. ACE, AGT vs. ATR1 and ACE vs. AGTR1, respectively. The positive interaction among the three genes and the risk of AMI had an odds ratio of 3.78 with a 95% CI of 0.88-12.85. CONCLUSIONS: The risk of developing AMI is higher whenever there are unfavorable alleles in gene-to-gene associations in the RAS.

Susceptibility to leprosy may be conditioned by an interaction between the NRAMP1 promoter polymorphisms and the lepromin response.

Controversial results have been achieved by attempting to associate the NRAMP1 gene with Mycobacterium leprae susceptibility as well as with the Mitsuda reaction, which represents a specific immune response to M. leprae. This study evaluated this association as well as the interaction of the polymorphism (GT)(n) in the promoter region of the NRAMP1 gene with a specific immune response to M. leprae measured by the intradermal Mitsuda test in leprosy patients and in non-consanguineous household contacts. The study aimed to evaluate the association of this gene polymorphism with resistance or susceptibility to the disease, and/or with clinical forms of the disease, in a population in an endemic area served by the State Reference Center in Sanitary Dermatology and Leprosy, Federal University of Uberlandia, MG, Brazil. Leprosy patients (90) were diagnosed according to Ridley and Jopling criteria and they grouped into multibacillary (MB) and paucibacillary (PB) patients. The control group consisted of 61 non-consanguineous contacts. NRAMP1 promoter genotypes were obtained through amplification by the polymerase chain reaction (PCR) followed by the detection through the low ionic-strength single strand conformational polymorphism (LIS-SSCP) electrophoretic technique. There were no significant differences in the allelic and genotypic frequencies for alleles 2, 3, and 4 in relation to the Mitsuda test among patients and household contacts, nor between those with MB and PB forms. However, individuals with a negative lepromin response associated with genotypes 22 and 23 presented a 7- and 8-fold greater chance of developing leprosy, respectively. Therefore, the NRAMP1 gene promoter polymorphism exhibited an interaction with the lepromin response, suggesting that allele 2 of the NRAMP1 promoter is an independent genetic factor that predisposes cells to enable pathogen survival, probably due to its low efficiency in iron transport. However, establishment of the infection and disease development may be conditioned by other immunological and genetic factors.